This report was generated using iSHARC.For additional downstream analyses and relevant tools, please refer to COBE.

Cells Composition per Sample

Number of cells and their cell cycle phase

Cells annotation

QC metrics across samples

Selected percentiles for QC metrics

  • nCount_RNA: The number of transcripts detected per cell.
  • pct_MT: The percentage of reads originating from the mitochondrial genes.
  • nCount_ATAC: The number of unique nuclear fragments.
  • TSS_Enrichment: The ratio of fragments centered at TSS to those in TSS-flanking regions.
  • Nucleosome_Signal: The approximate ratio of mononucleosomal to nucleosome-free fragments.
Total Number of cells across samples: 9593
nCount_RNA pct_MT nCount_ATAC TSS_Enrichment Nucleosome_Signal
0% 19.0 0.0000000 1.0 0.0158327 0.2727273
2.5% 109.0 0.0000000 19.0 0.7163071 0.6521549
25% 474.0 0.1944264 88.0 2.6223776 0.8614719
50% 808.0 0.6172840 203.0 3.3300033 0.9716312
75% 1422.0 1.4492754 438.0 4.2684588 1.0873239
97.5% 7780.4 4.7570082 1534.2 9.9900100 1.4065712
100% 47306.0 56.8181818 8995.0 37.3626374 2.6666667

Violin plots for selected QC metrics

Horizontally Integrated RNA

RNA integration across samples is performed using three approaches: simple merging, Harmony, and Seurat integration.The results are visualized below with cells labeled by sample ID (top panels) and clustering outcomes (bottom panels)

Horizontally Integrated ATAC

ATAC integration across samples is performed using three approaches: simple merging, Harmony, and Seurat integration.The results are visualized below with cells labeled by sample ID (top panels) and clustering outcomes (bottom panels)

vertically Integrated ATAC and RNA

WNN on top of harmony (top) and Seurat (bottom) integrated RNA and ATAC

RNA weights for WNN harmonized (top) and anchored (bottom) RNA and ATAC

Cell annotation distribution within each WNN-integrated cluster

Note: Cell annotations were assigned based on individual samples before integration of multiple samples.

List of main integrated outputs

Note: additional figures are available in the directory of : workdir/integrated_samples/!!

Differently integrated Seurat objects

  • rna/RNA_integrated_by_[merging | anchors | harmony].RDS: These are Seurat objects of horizontally integrated RNA across multiple samples by applying merge, Seurat, Harmony, respectively.
  • atac/ATAC_integrated_by_[merging | anchors | harmony].RDS: These are Seurat objects of horizontally integrated ATAC across multiple samples by applying merge, Seurat, Harmony, respectively.
  • wnn/harmony/RNA_ATAC_integrated_by_WNN.RDS: This Seurat object includes the vertically integrated RNA and ATAC across multiple sample after horizontally integrate each modality using Harmony.
  • wnn/achor/RNA_ATAC_integrated_by_WNN.RDS: This Seurat object includes the vertically integrated RNA and ATAC across multiple sample after horizontally integrate each modality using Seurat.

RMD file

  • Integrated_samples_QC_and_Primary_Results.Rmd: The Rmd file for generating this HTML report.